// Returns true if one or more files passed loads data into colour
bool graph_file_is_colour_loaded(size_t colour, const GraphFileReader *files,
size_t num_files)
{
size_t i;
for(i = 0; i < num_files; i++) {
if(file_filter_iscolloaded(&files[i].fltr, colour))
return true;
}
return false;
}
int ctx_correct(int argc, char **argv)
{
size_t i, j;
struct ReadThreadCmdArgs args = READ_THREAD_CMD_ARGS_INIT;
read_thread_args_alloc(&args);
read_thread_args_parse(&args, argc, argv, longopts, true);
GraphFileReader *gfile = &args.gfile;
PathFileBuffer *pfiles = &args.pfiles;
CorrectAlnInputBuffer *inputs = &args.inputs;
size_t ctx_total_cols = gfile->hdr.num_of_cols;
size_t ctx_num_kmers = gfile->num_of_kmers;
if(args.colour > ctx_total_cols)
cmd_print_usage("-c %zu is too big [> %zu]", args.colour, ctx_total_cols);
size_t ctp_usedcols = 0;
for(i = 0; i < pfiles->len; i++) {
if(!file_filter_iscolloaded(&pfiles->data[i].fltr, args.colour)) {
cmd_print_usage("Path file doesn't load into colour %zu: %s",
args.colour, pfiles->data[i].fltr.orig_path.buff);
}
ctp_usedcols = MAX2(ctp_usedcols, path_file_usedcols(&pfiles->data[i]));
}
//
// Decide on memory
//
size_t bits_per_kmer, kmers_in_hash, graph_mem, path_mem, total_mem;
// 1 bit needed per kmer if we need to keep track of noreseed
bits_per_kmer = sizeof(Edges)*8 + ctx_num_kmers + sizeof(uint64_t)*8;
kmers_in_hash = cmd_get_kmers_in_hash2(args.memargs.mem_to_use,
args.memargs.mem_to_use_set,
args.memargs.num_kmers,
args.memargs.num_kmers_set,
bits_per_kmer,
ctx_num_kmers, ctx_num_kmers,
false, &graph_mem);
// Paths memory
path_mem = path_files_mem_required(pfiles->data, pfiles->len, false, false,
ctp_usedcols, 0);
cmd_print_mem(path_mem, "paths");
// Total memory
total_mem = graph_mem + path_mem;
cmd_check_mem_limit(args.memargs.mem_to_use, total_mem);
//
// Check we can read all output files
//
// Open output files
SeqOutput *outputs = ctx_calloc(inputs->len, sizeof(SeqOutput));
bool output_files_exist = false;
for(i = 0; i < inputs->len; i++)
{
CorrectAlnInput *input = &inputs->data[i];
input->crt_params.ctxcol = input->crt_params.ctpcol = args.colour;
SeqOutput *output = &outputs[i];
seq_output_alloc(output);
seq_output_set_paths(output, input->out_base,
async_task_pe_output(&input->files));
input->output = output;
// output check prints warnings and returns true if errors
output_files_exist |= seq_output_files_exist_check(output);
}
// Abandon if some of the output files already exist
if(output_files_exist) die("Output files already exist");
// Attempt to open all files
for(i = 0; i < inputs->len && seq_output_open(&outputs[i]); i++) {}
// Check if something went wrong - if so remove all output files
if(i < inputs->len) {
for(j = 0; j < i; j++) seq_output_delete(&outputs[i]);
die("Couldn't open output files");
}
//
// Allocate memory
//
dBGraph db_graph;
db_graph_alloc(&db_graph, gfile->hdr.kmer_size, ctx_total_cols, 1, kmers_in_hash);
size_t bytes_per_col = roundup_bits2bytes(db_graph.ht.capacity);
db_graph.col_edges = ctx_calloc(db_graph.ht.capacity, sizeof(Edges));
db_graph.node_in_cols = ctx_calloc(bytes_per_col * ctx_total_cols, 1);
// Paths
path_store_alloc(&db_graph.pstore, path_mem, false,
db_graph.ht.capacity, ctp_usedcols);
//
// Load Graph and Path files
//
LoadingStats gstats = LOAD_STATS_INIT_MACRO;
GraphLoadingPrefs gprefs = {.db_graph = &db_graph,
.boolean_covgs = false,
.must_exist_in_graph = false,
.must_exist_in_edges = NULL,
.empty_colours = true};
// Load graph, print stats, close file
graph_load(gfile, gprefs, &gstats);
hash_table_print_stats_brief(&db_graph.ht);
graph_file_close(gfile);
// Load path files (does nothing if num_fpiles == 0)
paths_format_merge(pfiles->data, pfiles->len, false, false,
args.num_of_threads, &db_graph);
//
// Run alignment
//
correct_reads(args.num_of_threads, MAX_IO_THREADS,
inputs->data, inputs->len,
&db_graph);
// Close and free output files
for(i = 0; i < inputs->len; i++) seq_output_dealloc(&outputs[i]);
ctx_free(outputs);
read_thread_args_dealloc(&args);
db_graph_dealloc(&db_graph);
return EXIT_SUCCESS;
}
